Hi
i have tumor normal pairs and am interested in calling germline variants. The GATK UnifiedGenotyper does seem to call the germline variants as it does not require normal/tumor input arguments.
I don't think there are any options in GATK.
Apart from varscan2, what other tools can be used for germline calling based on tumor-normal pairs ?
And which one performs the best ?
i have tumor normal pairs and am interested in calling germline variants. The GATK UnifiedGenotyper does seem to call the germline variants as it does not require normal/tumor input arguments.
I don't think there are any options in GATK.
Apart from varscan2, what other tools can be used for germline calling based on tumor-normal pairs ?
And which one performs the best ?
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